Changeset 666e9e for src/Fragmentation

Timestamp:

May 7, 2016, 7:05:19 AM (9 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable

Children:

a9099d

Parents:

0ba27c9

git-author:

Frederik Heber <heber@…> (02/17/16 18:24:55)

git-committer:

Frederik Heber <heber@…> (05/07/16 07:05:19)

Message:

VMGFragmentController and FragmentationAutomationAction accept UseImplicitCharge.

• this causes nuclei charges for the full solution to be taken from the ParticleRegistry that contains partial charges table and not the elementary charges.

Location:

src/Fragmentation/Automation

Files:

• VMGFragmentController.cpp (modified) (4 diffs)
• VMGFragmentController.hpp (modified) (2 diffs)

src/Fragmentation/Automation/VMGFragmentController.cpp

@@ -47 +47 @@
 #include "Jobs/VMGJob.hpp"
 #include "molecule.hpp"
+#include "Potentials/Particles/Particle.hpp"
+#include "Potentials/Particles/ParticleRegistry.hpp"
 #include "World.hpp"
 
@@ -77 +79 @@
     const bool _DoPrintDebug,
     const bool _OpenBoundaryConditions,
-    const bool _DoSmearCharges)
+    const bool _DoSmearCharges,
+    const bool _UseImplicitCharges)
 {
   std::vector<FragmentJob::ptr> jobs;
@@ -110 +113 @@
   std::vector< std::vector<double> > positions;
   std::vector<double> charges;
+  const World &world = const_cast<const World &>(World::getInstance());
+  const ParticleRegistry &registry = const_cast<const ParticleRegistry &>(ParticleRegistry::getInstance());
   {
-    const World::ConstAtomComposite &atoms = const_cast<const World &>(World::getInstance()).
-        getAllAtoms();
+    const World::ConstAtomComposite &atoms = world.getAllAtoms();
     positions.reserve(atoms.size());
     charges.reserve(atoms.size());
@@ -118 +122 @@
     for (World::ConstAtomComposite::const_iterator iter = atoms.begin();
         iter != atoms.end(); ++iter) {
+      // set position for this atom
       const Vector &pos = (*iter)->getPosition();
       // convert positions to atomic length units
-      for (size_t i=0;i<3;++i) position[i] = pos[i]/AtomicLengthToAngstroem;
-      positions.push_back(position);
-      int charge = (*iter)->getElement().getAtomicNumber();
-      // subtract core electron charge from nuclei charge if only valence sampled
-      if (_DoValenceOnly == MPQCData::DoSampleValenceOnly)
-        charge -= getCoreElectrons(charge);
-      charges.push_back((double)charge);
+      for (size_t i=0;i<3;++i)
+        position[i] = pos[i]/AtomicLengthToAngstroem;
+
+      // use partial charges ...
+      const atomId_t atomid = (*iter)->getId();
+      if ((!world.isAtomSelected(atomid)) && (_UseImplicitCharges)) {
+        // ... for all unselected particles ...
+        const std::string &symbol = (*iter)->getElement().getSymbol();
+        if (registry.isPresentByName(symbol)) {
+          // ... that are present in ParticleRegistry
+          const Particle * const particle = registry.getByName(symbol);
+          LOG(3, "DEBUG: Using implicit charge " << particle->charge << " for atom " << atomid);
+          positions.push_back(position);
+          charges.push_back(particle->charge);
+        }
+      } else {
+        double charge = (*iter)->getElement().getAtomicNumber();
+        // subtract core electron charge from nuclei charge if only valence sampled
+        if (_DoValenceOnly == MPQCData::DoSampleValenceOnly)
+          charge -= getCoreElectrons(charge);
+        positions.push_back(position);
+        charges.push_back((double)charge);
+      }
     }
   }

src/Fragmentation/Automation/VMGFragmentController.hpp

@@ -64 +64 @@
    *        boundary conditions
    * \param _DoSmearCharges whether to smear out electronic charge distributions with bsplines or not
+   * \param _UseImplicitCharges use implicit charges in potential storage if
+   *            element is found
    */
   bool createLongRangeJobs(
@@ -75 +77 @@
       const bool _DoPrintDebug,
       const bool _OpenBoundaryConditions = false,
-      const bool _DoSmearCharges = false);
+      const bool _DoSmearCharges = false,
+      const bool _UseImplicitCharges = false);
 
   void waitforResults(const size_t NoExpectedResults)